Biomedical Research Core Facilities
Spring 2021 Newsletter
The Perelman School of Medicine is proud to support our integral research core facilities and research teams. Please stay safe and be well!
In this issue:

  • Announcements
  • Save the Date: Virtual Cores Day - September 30th, 2021
  • Invitation to Join PSOM ABRF Membership
  • Core Facilities Spotlight
  • Center for Advanced MRI & Spectroscopy (CAMRIS)
  • Extracelluar Vesicle Core Facility (Penn Vet)
  • Mixed Methods Research Laboratory
  • Penn Genomic Analysis Core Facility
  • OCRC Tumor BioTrust Collection
  • Stem Cell Xenograft Core Facility
Announcements - Save the Date: Virtual Cores Day - September 30, 2021
We are excited to welcome both new and returning core facilities to participate in this year’s virtual Cores Day! Please mark your calendars for Thursday, September 30th, 2021. New this year, the event will be held via the PheedLoop event management platform, with an aim to enrich and enhance the Cores Day experience for participants and attendees. 

The annual Cores Day event is a joint venture with CHOP, PSOM and Wistar, in an effort to showcase the many outstanding biomedical research resources and services available throughout our campus. This event is an opportunity for students, faculty, and staff to interface with a multitude of research core facilities via informational presentations provided by core facility personnel.  

Stay tuned for more details, and we hope to see you on Thursday, September 30th! 
Announcements - Invitation to Join PSOM ABRF Membership
The Perelman School of Medicine has recently obtained an institutional membership to the Association of Biomolecular Resource Facilities (ABRF).

ABRF maintains an active mailing list, frequently sharing information on a wide array of topics, surveys, and events that may be of interest to core facility directors. Recent examples include a Core Administrator Town Hall, a Diversity Equity & Inclusion Round Table Session, and an informative New Member Orientation.

The ABRF is a membership association with more than 700 members working in or providing support to resource and research biotechnology laboratories. Members represent hundreds of laboratories and administrative offices across government, academia, research, industry, and commercial settings. The ABRF promotes the education and career advancement of scientists through conferences, a quarterly journal, publication of research group studies and conference travel awards. The society also sponsors multi-center research studies designed to help members incorporate new biotechnologies into their laboratories.

We encourage you to visit the ABRF website (https://www.abrf.org/), and to contact April Weakley (aweakley@pennmedicine.upenn.edu) if you would like to the join the organization at no charge to you via our recently obtained organizational membership.
Device for MRI Scanner Intra-Bore Disinfection
Advantages
  • Low cost
  • Small size
  • Magnetic field safe
  • Rapid and effective disinfection
  • Easy set up and operation

Intellectual Property
  • Provisional application pending

Desired Partnerships
  • License
  • Co-development
Applications
  • Disinfection of bore for MRI and other types of scanners (CT, PET, PET-MR, SPECT)

Stage of Development
  • Built prototype
  • Confirmed effectiveness
‌
Technology Overview
Magnetic field-safe device for rapid disinfection of MRI bore and other types of scanners (CT, PET, PET-MR, SPECT) that is effective against COVID19, MRSA and other pathogens.

Problem
With the advent of Covid-19, renewed emphasis has been placed on disinfecting surfaces in the medical environment. Disinfecting the MRI scanner bore is of particular importance due to the substantial time the patient spends in the bore, the close contact between the patient and the bore, and continuous patient turnover. The scanner bore however presents a significant challenge to disinfect due to the strong magnet field and the space constraints imposed by the bore size and geometry. Also, for maximum effectiveness at controlling pathogen spread, disinfection of the bore must occur between each patient without disrupting the MRI schedule. Current method of disinfecting the bore involves the use of harsh chemicals manually applied by the MRI technician, which is inconsistent, time-consuming, and challenging to perform between patients due to scheduling constraints and MRI technician’s patient responsibilities. Additionally, the harsh chemical residues and fumes produced by the current method can corrode sensitive electronic systems as well as affect some patients.
Solution
To address the limitations of the current manual method of MRI bore disinfection, a device was developed that can rapidly and effectively disinfect this area using UV-C light. The device is specifically designed to use non-ferrous materials and shielding of the electronic components to eliminate magnetic field interference. The system produces an intensity of UV-C which disinfects the entire MRI bore within minutes, enables rapid setup and removal, eliminates the use of harsh chemicals, minimizes the MRI technician involvement, and provides the capability to rapidly and effectively disinfect the MRI bore between patients.
Learn More
Linara Axanova
Email: axanova@upenn.edu Phone: 215-573-3445
Docket No.: 20-9379
The Extracellular Vesicle Core Facility at PennVet has been hard at work to keep users engaged and active despite continued work restrictions due to SARS-CoV-2. Most recently, the facility was involved with and recently acknowledged in a publication from the laboratory of Dr. Serge Fuchs in the Journal of Clinical Investigations titled “Regulation of the intercellular biomolecule transfer-driven tumor angiogenesis and responses to anti-cancer therapies”.
 
Furthermore, facility director Dr. Rachel DeRita continues to foster collaboration and community growth through a biweekly webinar meeting among faculty and trainees involved in EV research. This meeting not only brings together fellow faculty but also is a means to connect with other core facilities and opportunities for funding new capital equipment that will elevate the local scientific community. For example, the EV Core and Imaging Core of Penn Vet, directed by Dr. Bruce Freedman, recently connected to gather faculty to collaborate on a large grant proposal to add Tau-STED capabilities to the Leica Stellaris FALCON microscope currently in use at the imaging facility. This new addition would allow nanoscale resolution of exosomes and other nanoparticles and protein complex interactions in live cells and therefore the ability to gain unprecedented insights into the biogenesis and uptake of exosomes, viruses and the use of nanoparticles as therapeutic agents. 
 
The EV Core facility is also in search of summer work study students, so those students interested in gaining additional laboratory experience in a rapidly growing field on the cutting edge of translational research, please contact Dr. DeRita at rmderita@upenn.edu.

For more updates about the EV Core facility and to submit services requests, please visit: https://www.vet.upenn.edu/research/core-resources-facilities/extracellular-vesicle-core
or contact rmderita@upenn.edu directly.  
Core Facilities Spotlight: Mixed Methods Research Laboratory
The Mixed Methods Research Lab is proud to announce publication of the below COVID-19 related research project in which they were involved.
Understanding Drivers of Coronavirus Disease 2019 Vaccine Hesitancy Among Blacks

Authors: Florence Momplaisir, Norrisa Haynes, Hervette Nkwihoreze, Maria N Nelson, Rachel M Werner, John Jemmott
Clinical Infectious Diseases, ciab102, https://doi.org/10.1093/cid/ciab102
 
This project utilized a mixed-methods, community engagement model to learn about factors contributing to vaccine hesitancy among Black West Philadelphia salon and barbershop owners and workers. Through a partnership with the Pennsylvania Personal Image Alliance (PPIA) and in connection with a University program meant to help community businesses safely reopen following their initial closure during the early months of the global COVID-19 pandemic, researchers conducted virtual focus groups with participants connected to the barbershop and salon industry in July and August 2020. While there was some variability in responses, the majority of participants were adamant that they would not be willing to take a COVID-19 vaccine, regardless of whether it was approved by the federal government. Specific vaccine-related concerns cited by participants included, safety, efficacy, misinformation, adverse side effects, the accelerated vaccine development timeline, and a distrust of the scientific and medical communities because of racist practices detrimental to Black participants and patients. Ultimately, participants felt that hearing accurate information from a trusted medical professional in their own life may increase their interest in taking a vaccine.
Core Facilities Spotlight: Penn Genomic Analysis Core Facility
The Penn Genomic Analysis Core (PGAC) provides investigators access to highest quality sequencing and molecular profiling technologies together with the scientific expertise necessary to utilize these technologies.
 
PGAC has been open throughout this pandemic. During first few months it has supported and continues to support COVID-19 and other essential research while maintaining all PSOM and EHRS protocols for laboratory work. It has been offering all services since July of last year.
 
Major Services Provided by the Core

1. Provide Consultation on sequencing and molecular profiling projects, perform Bioinformatic Analysis and, Software Training.

2. Next Generation Sequencing (NGS) on Illumina MiSeq & NextSeq 500 and Ion Torrent PGM & S5, including project design, library preparation and bioinformatic analyses

3. Sanger Sequencing on ABI capillary sequencers

4. Whole Genome & Targeted Molecular Profiling on Affymetrix GeneChips and high-throughput GeneTitan, Fluidigm BioMark HD, and ABI QS12 real-time PCR instruments
5. Fragment Analysis: Human Cell Line Authentication, Microsatellite-based Genotyping, SNaPshot, VNTR analysis

6. Molecular Biological Services: DNA & RNA preparation at different scales, Cloning, Sub-cloning, Site-directed Mutagenesis, Vector Construction

Project Highlights
 
Copy Number Variation (CNV) analysis from targeted NGS – In an ongoing project one group from PSOM is studying the relationship between glioblastoma tumor anatomical locations in the brain and tumor-associated mutations. The core designed a targeted sequencing panel suitable for FFPE DNA, of 45 genes, 4 additional mutation loci of interest and about 50 SNPs in chr. 1p and 19q. After sequencing on S5 sequencer bioinformatic analyses were performed to generate annotated and filtered somatic variant calls. The CNV calls were made with the help of CNVkit tool using as reference, DNA from 10 HapMap individuals screened for CNVs in the targeted region, after adjusting for tumor cellularity.
 
AAV vector sequencing - PGAC performs sequence verification of AAV Transfer, Helper and RepCap plasmids as well as final AAV viral vectors using NGS. Fragment libraries are prepared from plasmids and viral vector DNA and sequenced on an Illumina MiSeq generating 250bp paired end reads. AAV transfer plasmids and viral vector ITR sequences are subject to deletions, rearrangement and self-repair. During data analysis these events can confuse aligners and variant callers resulting in incorrect calls and, needs special care to evaluate the integrity of the ITR sequences. For viral vectors, the reads not aligned to the respective reference are screened against co-transfected plasmids as well as the human and E. coli genomes, Ad5 E1A gene, and any other sequences of interest to researchers.
 
Single guide RNA (sgRNA) sequencing – The sgRNAs (100b) were converted into cDNA and amplified by reverse transcription and template switching followed by PCR amplification of the cDNA. After purification by AMPure beads and quantitation on BioAnalyzer the PCR products were cloned and Sanger sequenced. Data analysis using Geneious software revealed a mixture of clones. A fraction of the clones had fully correct sequence, while others had the correct target -specific sequence but a few variants downstream. Some clones had variants also in the target.
 
Bioinformatics - John Tobias continues in his role of providing customized bioinformatics support for investigators at Penn and the broader research community. Recently, he contributed RNAseq and integrated ATACseq analyses to help elucidate the molecular mechanisms of Hutchinson-Gilford Progeria Syndrome, chemoresistance in breast cancer and, more generally, malignant transformation.
 
Selection of Recent Publications Co-authored by Core Members 
 
McAndrew, NP, Bottalico, L, Mesaros, C, Blair, IA, Tsao, PY, Rosado, JM, Ganguly, T, Song, SJ, Gimotty, PA, Mao, JJ, DeMichele, A. Effects of systemic inflammation on relapse in early breast cancer. npj Breast Cancer 7, 7 (2021). https://doi.org/10.1038/s41523-020-00212-6.
 
Pawlicki JM, Cookmeyer DL, Maseda D, Everett JK, Wei F, Kong H, Zhang Q, Wang HY, Tobias JW, Walter DM, Zullo KM, Javaid S, Watkins A, Wasik MA, Bushman FD, Riley JL. NPM-ALK induces reprogramming of mature TCR-stimulated T cells resulting in de-differentiation and malignant transformation. Cancer Res. 2021 Feb 22;. doi: 10.1158/0008-5472.CAN-20-2297. [Epub ahead of print] PubMed PMID: 33619116. 
 
Kumar S, Nandi A, Singh S, Regulapati R, Li N, Tobias JW, Siebel CW, Blanco MA, Klein-Szanto AJ, Lengner C, Welm AL, Kang Y, Chakrabarti R. Dll1+ quiescent tumor stem cells drive chemoresistance in breast cancer through NF-κB survival pathway. Nat Commun. 2021 Jan 18;12(1):432. doi: 10.1038/s41467-020-20664-5. PubMed PMID: 33462238; PubMed Central PMCID: PMC7813834.

Core Facilities Spotlight: OCRC Tumor BioTrust Collection
The Ovarian Cancer Research Center Tumor BioTrust Collection is open and continues to collect fresh cancer tissue specimens, as well as plasma, serum, peripheral blood mononuclear cells (PBMC), blood and other biological samples from various cancer cases with a focus on gynecologic cancers. We also house formalin fixed paraffin embedded (FFPE) samples including tissue microarray (TMA) construction and immunohistochemistry. Samples collected through the Penn Legacy Tissue Program (PLTP) (e.g., rapid autopsy) are also available and a quote can be provided upon request.

We will also work with investigators to prospectively collect specific samples to support their research within Penn research community as well as in outside academic institutions. We will be working with biotech/bio-pharma companies if it is within the confines of a collaboration.

We are excited to share the news that we recently welcomed Melissa Kelly, Director of Corporate Contracts, as a new member of the OCRC Tumor Advisory Committee, and she will provide help with navigating future requests and interactions, and it will be invaluable to get insights and contributions from PCI (Penn Center for Innovation) going forward. 
We are offering the following sample types:

  • Fresh Tumor Tissue
  • Frozen Tumor Tissue
  • Enzyme Digested Tumor Cells
  • Serum
  • Plasma
  • Peripheral Blood Mononuclear Cells (PBMC)
  • OCT
  • Formalin Fixed Paraffin Embedded (FFPE)
  • Tissue Microarray (TMA)
  • Samples from rapid autopsies

More info about the core and pricing can be found at: https://www.med.upenn.edu/OCRCBioTrust/
Representative Publications:
 
CAR-T cell-mediated depletion of immunosuppressive tumor-associated macrophages promotes endogenous antitumor immunity and augments adoptive immunotherapy.
Rodriguez-Garcia A, Lynn RC, Poussin M, Eiva MA, Shaw LC, O'Connor RS, Minutolo NG, Casado-Medrano V, Lopez G, Matsuyama T, Powell DJ Jr.
Nat Commun. 2021 Feb 9;12(1):877. doi: 10.1038/s41467-021-20893-2.
 
Inhibition of relaxin autocrine signaling confers therapeutic vulnerability in ovarian cancer.
Burston HE, Kent OA, Communal L, Udaskin ML, Sun RX, Brown KR, Jung E, Francis KE, La Rose J, Lowitz JK, Drapkin R, Mes-Masson AM, Rottapel R.
J Clin Invest. 2021 Feb 9:142677. doi: 10.1172/JCI142677.
 
Combining PARP with ATR inhibition overcomes PARP inhibitor and platinum resistance in ovarian cancer models.
Kim H, Xu H, George E, Hallberg D, Kumar S, Jagannathan V, Medvedev S, Kinose Y, Devins K, Verma P, Ly K, Wang Y, Greenberg RA, Schwartz L, Johnson N, Scharpf RB, Mills GB, Zhang R, Velculescu VE, Brown EJ, Simpkins F.
Nat Commun. 2020 Jul 24;11(1):3726. doi: 10.1038/s41467-020-17127-2.
 
PARP Theranostic Auger Emitters Are Cytotoxic in BRCA Mutant Ovarian Cancer and Viable Tumors from Ovarian Cancer Patients Enable Ex-Vivo Screening of Tumor Response. Molecules.
Riad A, Gitto SB, Lee H, Winters HD, Martorano PM, Hsieh CJ, Xu K, Omran DK, Powell DJ Jr, Mach RH, Makvandi M.
2020 Dec 19;25(24):6029. doi: 10.3390/molecules25246029.
 
An autologous humanized patient-derived-xenograft platform to evaluate immunotherapy in ovarian cancer
Sarah B. Gitto, Hyoung Kim, Stavros Rafail, Dalia K. Omran, Sergey Medvedev, Yasuto Kinose, Alba Rodriguez-Garcia, Ahron J. Flowers, Haineng Xu, Lauren E. Schwartz, Daniel J. Powell Jr., Fiona Simpkins
Gynecologic Oncology 156 (2020) 222e232.
 
CAR T Cells Targeting MISIIR for the Treatment of Ovarian Cancer and Other Gynecologic Malignancies
Alba Rodriguez-Garcia, Prannda Sharma, Mathilde Poussin, Alina C. Boesteanu, Nicholas G. Minutolo, Sarah B. Gitto, Dalia K. Omran, Matthew K. Robinson, Gregory P. Adams, Fiona Simpkins, and Daniel J. Powell, Jr.
Molecular Therapy (2019), https://doi.org/10.1016/j.ymthe.2019.11.028.
 
Imaging Collagen Alterations in STICs and High Grade Ovarian Cancers in the Fallopian Tubes by Second Harmonic Generation Microscopy
Eric C. Rentchler, Kristal L. Gant, Ronny Drapkin, Manish Patankar and Paul J. Campagnola,*
Cancers 2019, 11, 1805; doi:10.3390/cancers11111805.
 
CD105 Is Expressed in Ovarian Cancer Precursor Lesions and Is Required for Metastasis to the Ovary
Shoumei Bai, Wanhong Zhu, Lan Coffman, Anda Vlad, Lauren E. Schwartz, Esther Elishaev, Ronny Drapkin and Ronald J Buckanovich
Cancers 2019, 11, 1710; doi:10.3390/cancers11111710.
 
Innervation of cervical carcinoma is mediated by cancer-derived exosomes
Christopher T. Lucido, Emily Wynja, Marianna Madeoa, Caitlin S.Williamson, Lauren E. Schwartz, Brittney A. Imblumc, Ronny Drapkin, Paola D. Vermeer
Gynecol Oncol. 2019 Jul;154(1):228-235.
Contact Us
Ovarian Cancer Research Center Tumor BioTrust Collection
Ehay Jung, Technical Director
Smilow CTR 08-191A
3400 Civic Center Blvd
Philadelphia, PA 19104
Phone: 215-746-5137
Core Facilities Spotlight: Stem Cell and Xenograft Core Facility
Recipient Of The First Conscientious Investigator Award
 
In 2021, The University Animal Resources (ULAR) and The Office of Animal Welfare (OAW) created the first Conscientious Investigator Award (https://iacuc.upenn.edu/other-resources/conscientious-investigators-award).
 
This award acknowledges laboratories and individuals who “go above and beyond to ensure that their animals (rodents and non-rodents) are cared for, that innovate in the name of animal welfare in research, and that proactively work with ULAR, the OAW, and the IACUC to achieve these goals.”
 
ULAR and OAW reviewed nominations from the Penn Research Community and gave the first Conscientious Investigator Award to the Stem Cell and Xenograft Core (https://www.med.upenn.edu/scxc/), more specifically the Xenograft / In Vivo Services Team, for its work with rodents (https://iacuc.upenn.edu/other-resources/conscientious-investigators-award/2021-award-winners).
   
The Xenograft / In Vivo Services team (https://www.med.upenn.edu/scxc/xenograft.html) from the SCXC is managed by Anthony Secreto, M.R.A., and is composed of three talented individuals, Joshua Glover, Derrick Dopkin and Eric Balboa.
 
ULAR and OAW acknowledged that the SCXC “constantly strives to improve the care and handling of the immunocompromised mice in their charge. They are in regular contact with ULAR and the OAW to ensure compliance and propose refinements and overall improvements to their program. They also share their knowledge and expertise on both research related techniques and animal handling with other investigators and strive to raise the standards for research on immunocompromised mice campus-wide.”
 
Most importantly, ULAR and OAW recognized that “The integrity of the SCXC is beyond measure from the training to the communication with management. They are passionate about what they do and continue to find ways to get even better.”
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